I am working with WES data and I am trying to build a pipeline with the help of GATK best practices. I would like to know the difference between pipeline that is built-in in Illumina sequencer and GATk Best Practices pipeline.
Is the VQSR used in built in software of Illumina? Why should I follow Best practices when everything is built in sequencer, can you please help me to see the difference?
Thank you very much